Access the full text.
Sign up today, get DeepDyve free for 14 days.
D. Conrad, D. Pinto, R. Redon, L. Feuk, O. Gokcumen, Yujun Zhang, J. Aerts, Peter Campbell, Tomas Fitzgerald, C. Ihm, K. Kristiansson, J. MacDonald, Ifejinelo Onyiah, Andy Chun, S. Robson, K. Stirrups, A. Valsesia, Klaudia Walter, John Wei, C. Tyler-Smith, N. Carter, Charles Lee, S. Scherer, M. Hurles (2010)
Origins and functional impact of copy number variation in the human genomeNature, 464
A. Valente, Seth Roberts, G. Buck, Yuan Gao (2009)
Functional organization of the yeast proteome by a yeast interactome mapProceedings of the National Academy of Sciences, 106
T. Gandhi, Jun Zhong, S. Mathivanan, L. Karthick, K. Chandrika, S. Mohan, Salil Sharma, Stefan Pinkert, S. Nagaraju, Balamurugan Periaswamy, Goparani Mishra, Kannabiran Nandakumar, Beiyi Shen, Nandan Deshpande, R. Nayak, M. Sarker, J. Boeke, G. Parmigiani, J. Schultz, J. Bader, A. Pandey (2006)
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasetsNature Genetics, 38
S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M. Ferreira, David Bender, J. Maller, P. Sklar, P. Bakker, M. Daly, P. Sham (2007)
PLINK: a tool set for whole-genome association and population-based linkage analyses.American journal of human genetics, 81 3
T. Mackay, R. Anholt (2006)
Of flies and man: Drosophila as a model for human complex traits.Annual review of genomics and human genetics, 7
J. Flint, T. Mackay (2009)
Genetic architecture of quantitative traits in mice, flies, and humans.Genome research, 19 5
K. Pattin, J. Moore (2008)
Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseasesHuman Genetics, 124
N. Iwai, S. Baba, T. Mannami, T. Ogihara, J. Ogata (2001)
Association of a Sodium Channel α Subunit Promoter Variant with Blood PressureJournal of The American Society of Nephrology, 13
B. Boeve, D. Maraganore, J. Parisi, R. Ivnik, B. Westmoreland, D. Dickson, M. Hutton, J. Hardy, R. Caselli, R. Petersen (2002)
Corticobasal Degeneration and Frontotemporal Dementia Presentations in a Kindred with Nonspecific HistopathologyDementia and Geriatric Cognitive Disorders, 13
C. Herold, M. Steffens, F. Brockschmidt, M. Baur, T. Becker (2009)
INTERSNP: genome-wide interaction analysis guided by a priori informationBioinformatics, 25 24
M. Mehdy, D. Ratner, R. Firtel (1983)
Induction and modulation of cell-type-specific gene expression in dictyosteliumCell, 32
K. Tarassov, Vincent Messier, C. Landry, S. Radinovic, M. Molina, I. Shames, Yelena Malitskaya, J. Vogel, H. Bussey, S. Michnick (2008)
An in Vivo Map of the Yeast Protein InteractomeScience, 320
J. Kroymann, T. Mitchell-Olds (2005)
Epistasis and balanced polymorphism influencing complex trait variationNature, 435
Chris Stark, B. Breitkreutz, T. Reguly, Lorrie Boucher, A. Breitkreutz, M. Tyers (2005)
BioGRID: a general repository for interaction datasetsNucleic Acids Research, 34
Bin Xu, J. Roos, S. Levy, E. Rensburg, J. Gogos, M. Karayiorgou (2008)
Strong association of de novo copy number mutations with sporadic schizophreniaNature Genetics, 40
C. Palmer, M. Diehn, Ash Alizadeh, P. Brown (2006)
Cell-type specific gene expression profiles of leukocytes in human peripheral bloodBMC Genomics, 7
T. Ravasi, Harukazu Suzuki, C. Cannistraci, S. Katayama, V. Bajic, Kai Tan, A. Akalin, S. Schmeier, M. Kanamori-Katayama, N. Bertin, Piero Carninci, C. Daub, A. Forrest, J. Gough, S. Grimmond, Jung-Hoon Han, Takehiro Hashimoto, Winston Hide, Oliver Hofmann, A. Kamburov, M. Kaur, H. Kawaji, A. Kubosaki, T. Lassmann, E. Nimwegen, C. MacPherson, Chihiro Ogawa, A. Radovanovic, Ariel Schwartz, R. Teasdale, J. Tegnér, B. Lenhard, S. Teichmann, T. Arakawa, N. Ninomiya, Kayoko Murakami, M. Tagami, S. Fukuda, K. Imamura, C. Kai, R. Ishihara, Yayoi Kitazume, J. Kawai, D. Hume, T. Ideker, Y. Hayashizaki (2010)
An Atlas of Combinatorial Transcriptional Regulation in Mouse and ManCell, 140
N. Iwai, S. Baba, T. Mannami, T. Ogihara, J. Ogata (2002)
Association of a sodium channel alpha subunit promoter variant with blood pressure.Journal of the American Society of Nephrology : JASN, 13 1
A. Singleton, M. Farrer, J. Johnson, A. Singleton, S. Hague, J. Kachergus, M. Hulihan, T. Peuralinna, A. Dutra, R. Nussbaum, S. Lincoln, A. Crawley, M. Hanson, D. Maraganore, C. Adler, Michael Cookson, M. Muenter, M. Baptista, D. Miller, J. Blancato, J. Hardy, K. Gwinn‐Hardy (2003)
α-Synuclein Locus Triplication Causes Parkinson's DiseaseScience, 302
S. Mccarroll, A. Huett, Petric Kuballa, S. Chilewski, Aimee Landry, P. Goyette, M. Zody, Jennifer Hall, S. Brant, Judy Cho, R. Duerr, M. Silverberg, K. Taylor, J. Rioux, D. Altshuler, M. Daly, R. Xavier (2008)
Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's diseaseNature Genetics, 40
R. Fisher
XV.—The Correlation between Relatives on the Supposition of Mendelian Inheritance.Transactions of the Royal Society of Edinburgh, 52
P. Phillips (2008)
Epistasis — the essential role of gene interactions in the structure and evolution of genetic systemsNature Reviews Genetics, 9
J. Moore, Scott Williams (2009)
Epistasis and its implications for personal genetics.American journal of human genetics, 85 3
P. Pagel, Stefan Kovac, Matthias Oesterheld, Barbara Brauner, I. Dunger, Goar Frishman, Corinna Montrone, Pekka Mark, V. Stümpflen, H. Mewes, A. Ruepp, D. Frishman (2005)
The MIPS mammalian protein?Cprotein interaction databaseBioinformatics, 21 6
Yu Zhang, Jun Liu (2007)
Bayesian inference of epistatic interactions in case-control studiesNature Genetics, 39
N. Krogan, G. Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, A. Ignatchenko, Joyce Li, S. Pu, Nira Datta, A. Tikuisis, Thanuja Punna, J. Peregrín-Alvarez, M. Shales, Xin Zhang, Michael Davey, M. Robinson, Alberto Paccanaro, J. Bray, Anthony Sheung, B. Beattie, D. Richards, Veronica Canadien, A. Lalev, Frank Mena, Peter Wong, A. Starostine, Myra Canete, James Vlasblom, Samuel Wu, Chris Orsi, Sean Collins, Shamanta Chandran, R. Haw, J. Rilstone, Kiran Gandi, Natalie Thompson, Gabriel Musso, P. Onge, S. Ghanny, M. Lam, G. Butland, Amin Altaf-Ul, S. Kanaya, A. Shilatifard, E. O’Shea, J. Weissman, C. Ingles, T. Hughes, J. Parkinson, M. Gerstein, S. Wodak, A. Emili, J. Greenblatt (2006)
Global landscape of protein complexes in the yeast Saccharomyces cerevisiaeNature, 440
Maya Kasowski, Fabian Grubert, Christopher Heffelfinger, M. Hariharan, A. Asabere, S. Waszak, L. Habegger, J. Rozowsky, Minyi Shi, A. Urban, Miyoung Hong, K. Karczewski, W. Huber, S. Weissman, M. Gerstein, J. Korbel, Michael Snyder (2010)
Variation in Transcription Factor Binding Among HumansScience, 328
J. Korn, F. Kuruvilla, S. Mccarroll, Alec Wysoker, J. Nemesh, S. Cawley, E. Hubbell, Jim Veitch, P. Collins, K. Darvishi, Charles Lee, Marcia Nizzari, S. Gabriel, S. Purcell, M. Daly, D. Altshuler (2008)
Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVsNature Genetics, 40
C. Ng, K. Koyama, S. Okamura, H. Kondoh, Y. Takei, Yusuke Nakamura (1999)
Isolation and characterization of a novel TP53‐inducible gene, TP53TG3Genes, 26
U. Stelzl, U. Worm, M. Lalowski, Christian Haenig, F. Brembeck, H. Goehler, Martin Stroedicke, Martina Zenkner, Anke Schoenherr, Susanne Koeppen, Jan Timm, Sascha Mintzlaff, C. Abraham, Nicole Bock, S. Kietzmann, A. Goedde, Engin Toksöz, A. Droege, S. Krobitsch, B. Korn, W. Birchmeier, H. Lehrach, E. Wanker (2005)
A Human Protein-Protein Interaction Network: A Resource for Annotating the ProteomeCell, 122
Jennifer Stone, M. O’Donovan, H. Gurling, G. Kirov, Douglas Blackwood, A. Corvin, N. Craddock, M. Gill, Christina Hultman, Paul Lichtenstein, A. McQuillin, C. Pato, D. Ruderfer, M. Owen, D. Clair, Patrick Sullivan, P. Sklar, S. Purcell, Joshua Korn, Stuart Macgregor, Derek Morris, C. O’Dushlaine, Mark Daly, P. Visscher, P. Holmans, E. Scolnick, Nigel Williams, Lucy Georgieva, I. Nikolov, Nadine Norton, H. Williams, D. Toncheva, V. Milanova, E. Thelander, Patrick Sullivan, E. Kenny, J. Waddington, K. Choudhury, S. Datta, J. Pimm, S. Thirumalai, V. Puri, R. Krasucki, J. Lawrence, D. Quested, N. Bass, David Curtis, C. Crombie, Gillian Fraser, Soh Kwan, N. Walker, Walter Muir, K. McGhee, Ben Pickard, P. Malloy, A. Maclean, Margaret Beck, M. Pato, H. Medeiros, Frank Middleton, C. Carvalho, C. Morley, A. Fanous, David Conti, James Knowles, Carlos Ferreira, A. Macedo, M. Azevedo, Steve McCarroll, K. Chambert, Casey Gates, S. Gabriel, Scott Mahon, Kristen Ardlie (2008)
Rare chromosomal deletions and duplications increase risk of schizophreniaNature, 455
M. Whitfield, D. Finlay, J. Murray, O. Troyanskaya, J. Chi, Alexander Pergamenschikov, T. McCalmont, P. Brown, D. Botstein, D. Botstein, M. Connolly (2003)
Systemic and cell type-specific gene expression patterns in scleroderma skinProceedings of the National Academy of Sciences of the United States of America, 100
T. Manolio, F. Collins, N. Cox, D. Goldstein, L. Hindorff, D. Hunter, M. McCarthy, E. Ramos, L. Cardon, A. Chakravarti, Judy Cho, A. Guttmacher, A. Kong, L. Kruglyak, E. Mardis, C. Rotimi, M. Slatkin, David Valle, A. Whittemore, M. Boehnke, A. Clark, E. Eichler, G. Gibson, J. Haines, T. Mackay, S. Mccarroll, P. Visscher (2009)
Finding the missing heritability of complex diseasesNature, 461
H. Cordell (2009)
Detecting gene–gene interactions that underlie human diseasesNature Reviews Genetics, 10
Yan Sun, P. Peyser, S. Kardia (2009)
A Common Copy Number Variation on Chromosome 6 Association With the Gene Expression Level of Endothelin 1 in Transformed B Lymphocytes From Three Racial GroupsCirculation: Cardiovascular Genetics, 2
K. Harvey, A. Dinudom, D. Cook, Sharad Kumar (2001)
The Nedd4-like Protein KIAA0439 Is a Potential Regulator of the Epithelial Sodium Channel*The Journal of Biological Chemistry, 276
A. Singleton, M. Farrer, J. Johnson, A. Singleton, S. Hague, J. Kachergus, M. Hulihan, T. Peuralinna, A. Dutra, R. Nussbaum, S. Lincoln, A. Crawley, M. Hanson, D. Maraganore, C. Adler, M. Cookson, M. Muenter, M. Baptista, D. Miller, J. Blancato, J. Hardy, K. Gwinn‐Hardy (2003)
alpha-Synuclein locus triplication causes Parkinson's disease.Science, 302 5646
L. Penrose
THE CORRELATION BETWEEN RELATIVES ON THE SUPPOSITION OF MENDELIAN INHERITANCE
L. Steinmetz, Himanshu Sinha, D. Richards, Jamie Spiegelman, P. Oefner, J. McCusker, Ronald Davis (2002)
Dissecting the architecture of a quantitative trait locus in yeastNature, 416
M. Ritchie, L. Hahn, N. Roodi, L. Bailey, W. Dupont, F. Parl, J. Moore (2001)
Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer.American journal of human genetics, 69 1
Jennifer Smith, S. Turner, Yan Sun, M. Fornage, Reagan Kelly, T. Mosley, C. Jack, I. Kullo, S. Kardia (2008)
Complexity in the genetic architecture of leukoaraiosis in hypertensive sibships from the GENOA StudyBMC Medical Genomics, 2
A. Tong, G. Lesage, Gary Bader, Huiming Ding, Hong Xu, Xiaofeng Xin, J. Young, G. Berriz, Renée Brost, Michael Chang, Yiqun Chen, X. Cheng, G. Chua, H. Friesen, D. Goldberg, J. Haynes, Christine Humphries, Grace He, Shamiza Hussein, Lizhu Ke, N. Krogan, Zhijian Li, J. Levinson, Hong Lu, Patrice Ménard, Christella Munyana, A. Parsons, Owen Ryan, Raffi Tonikian, T. Roberts, A. Sdicu, Jesse Shapiro, Bilal Sheikh, B. Suter, Sharyl Wong, Lan Zhang, Hongwei Zhu, C. Burd, S. Munro, C. Sander, J. Rine, J. Greenblatt, M. Peter, A. Bretscher, G. Bell, F. Roth, Grant Brown, B. Andrews, H. Bussey, Charles Boone (2004)
Global Mapping of the Yeast Genetic Interaction NetworkScience, 303
A. Price, N. Patterson, R. Plenge, M. Weinblatt, N. Shadick, D. Reich (2006)
Principal components analysis corrects for stratification in genome-wide association studiesNature Genetics, 38
Toshihiro Tanaka (2003)
The International HapMap ProjectNature, 426
T. Walsh, J. McClellan, S. McCarthy, A. Addington, S. Pierce, G. Cooper, A. Nord, M. Kusenda, D. Malhotra, A. Bhandari, S. Stray, C. Rippey, P. Roccanova, Vladimir Makarov, B. Lakshmi, R. Findling, L. Sikich, T. Stromberg, B. Merriman, N. Gogtay, P. Butler, K. Eckstrand, L. Noory, P. Gochman, R. Long, Zugen Chen, S. Davis, Carl Baker, E. Eichler, P. Meltzer, S. Nelson, A. Singleton, Ming Lee, J. Rapoport, M. King, J. Sebat (2008)
Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in SchizophreniaScience, 320
J. Sebat, B. Lakshmi, D. Malhotra, J. Troge, Christa Lese-Martin, T. Walsh, B. Yamrom, Seungtai Yoon, A. Krasnitz, J. Kendall, A. Leotta, D. Pai, Ray Zhang, Yoon-ha Lee, J. Hicks, S. Spence, Annette Lee, K. Puura, T. Lehtimäki, D. Ledbetter, P. Gregersen, J. Bregman, J. Sutcliffe, V. Jobanputra, W. Chung, D. Warburton, M. King, D. Skuse, D. Geschwind, T. Gilliam, Kenny Ye, M. Wigler (2007)
Strong Association of De Novo Copy Number Mutations with AutismScience, 316
M. Sowa, E. Bennett, S. Gygi, J. Harper (2009)
Defining the Human Deubiquitinating Enzyme Interaction LandscapeCell, 138
M. Costanzo, A. Baryshnikova, J. Bellay, Yungil Kim, Eric Spear, C. Sevier, Huiming Ding, J. Koh, Kiana Toufighi, S. Mostafavi, Jeany Prinz, R. Onge, Benjamin VanderSluis, Taras Makhnevych, F. Vizeacoumar, Solmaz Alizadeh, S. Bahr, Renée Brost, Yiqun Chen, Murat Cokol, R. Deshpande, Zhijian Li, Zhen-Yuan Lin, Wendy Liang, M. Mårback, Jadine Paw, Bryan-Joseph Luis, Ermira Shuteriqi, A. Tong, Nydia Dyk, Iain Wallace, J. Whitney, M. Weirauch, Guoqing Zhong, Hongwei Zhu, W. Houry, M. Brudno, Sasan Ragibizadeh, Balázs Papp, C. Pál, F. Roth, G. Giaever, C. Nislow, O. Troyanskaya, H. Bussey, Gary Bader, A. Gingras, Q. Morris, Philip Kim, C. Kaiser, C. Myers, B. Andrews, Charles Boone (2010)
The Genetic Landscape of a CellScience, 327
J. Wolf, E. Brodie, M. Wade (2000)
Epistasis and the Evolutionary Process
K. Pattin, J. Moore (2009)
Role for protein–protein interaction databases in human geneticsExpert Review of Proteomics, 6
W. Bateson (1910)
Mendel's Principles of HeredityThe Indian Medical Gazette, 45
B. Stranger, M. Forrest, M. Dunning, Catherine Ingle, C. Beazley, N. Thorne, R. Redon, C. Bird, A. Grassi, Charles Lee, C. Tyler-Smith, N. Carter, S. Scherer, S. Tavaré, P. Deloukas, M. Hurles, E. Dermitzakis (2007)
Relative Impact of Nucleotide and Copy Number Variation on Gene Expression PhenotypesScience, 315
L. Weiss, Yiping Shen, J. Korn, D. Arking, David Miller, R. Fossdal, E. Saemundsen, H. Stefánsson, M. Ferreira, Todd Green, O. Platt, D. Ruderfer, C. Walsh, D. Altshuler, A. Chakravarti, R. Tanzi, K. Stefánsson, S. Santangelo, J. Gusella, P. Sklar, Bai-Lin Wu, M. Daly (2008)
Association between microdeletion and microduplication at 16p11.2 and autism.The New England journal of medicine, 358 7
Epistasis (i.e. genegene interaction) has long been recognized as an important mechanism underlying the complexity of the genetic architecture of human traits. Definitions of epistasis range from the purely molecular to the traditional statistical measures of interaction. The statistical detection of epistasis usually does not map onto or easily relate to the biological interactions between genetic variations through their combined influence on gene expression or through their interactions at the gene product (i.e. protein) or DNA level. Recently, greater high-dimensional data on proteinprotein interaction (PPI) and gene expression profiles have been collected that enumerates sets of biological interactions. To better align statistical and molecular models of epistasis, we present an example of how to incorporate the PPI information into the statistical analysis of interactions between copy number variations (CNVs). Among the 23 640 pairs of known human PPIs and the 1141 common CNVs detected among HapMap samples, we identified 37 pairs of CNVs overlapping with both genes of a PPI pair. Two CNV pairs provided sufficient genotype variation to search for epistatic effects on gene expression. Using 47 294 probe-specific gene expression levels as the outcomes, five epistatic effects were identified with P-value less than 106. We found a CNVCNV interaction significantly associated with gene expression of TP53TG3 (P-value of 2 1020). The proteins associated with the CNV pair also bind TP53 which regulates the transcription of TP53TG3. This study demonstrates that using PPI data can assist in targeting statistical hypothesis testing to biological plausible epistatic interaction that reflects molecular mechanisms.
Human Molecular Genetics – Oxford University Press
Published: Nov 15, 2010
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.